Visualizing PubMed

There are a number of sites where you can do a PubMed search and display the results in interesting and sometimes quirky ways.

Here is a KNAKIJ search on low back pain[mh] AND laser therapy, low level[mh]. You can click on the circles and link to PubMed records.

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Here are some of these visualizing sites:

  • PubMed PubReMiner
    PubReMiner is a front-end for the popular PubMed literature database at the NCBI. When you submit your query (which can be any query that can be processed by PubMed), PubReMiner will process the result of that query and display its results (in the form of selectable “keywords”) in frequency tables, which can be added/excluded from the query to optimize the results.
  • KNAKIJ – information visualization
    KNALIJ PubMed: KNALIJ is a real-time infographic engine. The KNALIJ PubMed web application is built to visualize and explore the connections within medical research. KNALIJ PubMed draws upon more than 22 million abstracts as a unique knowledge discovery tool  More
  • LigerCat: Literature and Genomics Resource Catalogue
    Search PubMed using words or even a DNA/protein sequence to create a tag cloud showing an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, combining the associated MeSH descriptors into a cloud, weighted by frequency.
  • Genes2WordCloud [Click on PUBMED SEARCH]
    Create Word Clouds using PubMed searches  Help

The new, improved PubMed

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On September 30, NCBI mounted the preview site for the redesigned PubMed. When I first looked at it, I thought they had omitted some key resources like the MeSH and Journals Databases. But I think I entered the site just as they were putting it up, and today, on October 1, there are some great features on the site.

Check out this record:  http://preview.ncbi.nlm.nih.gov/pubmed/17142167

The default display is now Abstract, with links to the MeSH terms/Publication Types and LinkOut directly below each record. I had heard a rumour that they were going to eliminate the Single Citation Matcher, but apparently there was an uproar among librarians (a terrifying thought) and the feature was retained. There is a simple search and an Advanced Search, and links to the PubMed Tools and More Resources are right on the home page. I think this is an improvement on the current site, where the only way to see MeSH terms is to use the Citation Display. This was not intuitive, and now all users will be able to view the MeSH terms easily.

Read more about the redesign in the September-October 2009 NLM Technical Bulletin.


The Internet Archive

Internet_Archive   Most people now know about the Internet Archive, but it’s always worth a reminder, it’s such a great resource. This is where you can look at Moving Images, Live Music Archive, Audio and Texts and, of course, the Wayback Machine. ( An example from the Live Music ArchiveGrateful Dead Live at Adams Field House, U of Montana on 1974-05-14.)

From the site: The Internet Archive, a 501(c)(3) non-profit, is building a digital library of Internet sites and other cultural artifacts in digital form. Like a paper library, we provide free access to researchers, historians, scholars, and the general public

Through the Wayback Machine you can track the development of Web sites, back to the mid-90s in some cases:
The Wayback Machine is a 150 billion page web archive with a front end to serve it through the archive.org website.
” … we got a nice letter from the last living director of the Rocky and Bullwinkle Show, Gerard Baldwin, because he read about the “fantastic project”. Our Wayback Machine is a tribute to their more cleverly named “Waybac Machine” which in turn was a reference to the Univac. Sherman and Peabody live on.”  Wikipedia entry    Archive of cnn.com

Here are the Internet Archives’ Frequently Asked Questions, and their blog, What’s New at the Internet Archive.


World Digital Library – April 2009

Here is a fantastic new resource, the World Digital Library , which just launched in April 2009. It makes available on the Internet, free of charge and in multilingual format, significant primary materials from cultures around the world, and includes manuscripts, maps, books, musical scores, recordings, films, prints, and photographs. You can browse by place, time, topic, type of item, or institution. The Library was developed by a team at the U.S. Library of Congress, with contributions by national libraries and with the support of UNESCO, companies and private foundations. (Google contributed $3 million.)

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More from the About page:
U.S. Librarian of Congress James H. Billington proposed the establishment of the WDL in a speech to the U.S. National Commission for UNESCO in June 2005. The basic idea was to create an Internet-based, easily-accessible collection of the world’s cultural riches that would tell the stories and highlight the achievements of all countries and cultures, thereby promoting cross-cultural awareness and understanding. UNESCO welcomed the idea as a contribution toward fulfilling UNESCO’s strategic objectives, which include promoting knowledge societies, building capacity in developing countries, and promoting cultural diversity on the Web. UNESCO Director-General Koichiro Matsuura designated UNESCO’s Directorate for Communication and Information, led by Dr. Abdul Waheed Khan, to work with the Library of Congress to develop the project.

The Cochrane Library is now free for all Canadians!

cclogo.gif  About a year ago, I wrote a blog post entitled Cochrane Library: Free access for all?  Well, this has come to Canada, as a pilot project.  The Canadian Cochrane Network and Centre announced on April 15 that everyone in Canada is now able to access the full contents of the Cochrane Library. From the announcement:

The Canadian Cochrane Network and Centre, in partnership with the Canadian Health Libraries Association, has successfully secured a national license to The Cochrane Library. In essence, the license provides a subscription for every Canadian with access to the Internet to benefit from the immense volume of health information found in The Cochrane Library. Everybody will be one click away from the best available evidence on the effectiveness of treatment procedures including which ones may be harmful.

Access the Cochrane Library at http://www.thecochranelibrary.com.


Canadian Association of Continuing Health Education (CACHE) Web Site

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Welcome to the latest version of the Web site of the Canadian Association of Continuing Health Education/Association canadienne d’éducation médicale continue (CACHE/ACEMC)!  This site has been around for a number of years, and was created by Fred Murray of Calgary, Alberta.  CACHE/ACEMC recently hired Dave Jackson, also of Calgary, who has mounted the site on Joomla, an Open Source content management system.

There is lots of content now, and I invite you to view in particular the Web Resources and Online Library sections.

Dave has created a search system in Joomla whereby you can search the links we place on our site, as well as the content of those off-site links.  This is quite extraordinary and provides medical educators with a rich collection of Web resources.

The Online Library is equally outstanding. The question I get most in my work is, “But where is the full text of the article?”  So I decided to create a library of free, full text articles, arranged in such categories as Effectiveness of Continuing Health Education; Physician Competence; Health Provider / Industry Relationship; Reflection in Learning/Thinking/Teaching/Practice; Knowledge Translation: Research into Practice; Internet Continuing Health Education; Evidence-Based Health Care; Rural Health; Journal Impact Factor … and more. Wherever possible there are links to PubMed records, so that users can use PubMed’s Related Articles feature to locate further publications.

This Web site has a decidedly Canadian flavour, but I think there is much of interest here for all medical educators. Soon a parallel French version will be up and running. Do pay us a visit, and be prepared to learn!


LIFE Photo Archive through Google

anne_charles_small  When I was young, my family’s subscriptions included the Globe and Mail, the Toronto Telegram, The New Yorker and LIFE magazine. The newspapers were of interest to me mainly for their comics, particularly the coloured ones that were delivered on the weekend. The stories in The New Yorker (delivered on Saturdays – we still had Saturday mail delivery in those days) helped nurture my lifelong love of literature. But it was the pictures in LIFE that captured my imagination, from those early ones of my namesake Anne and her brother Charles (the picture above is from 1954), to the spreads on the young Senator Kennedy and his beautiful wife with her little round hats, to the scary coverage of the Cuban Missile Crisis. And, of course, I loved all those shots of such notables as Marilyn Monroe and Elvis Presley and The Beatles. (They’re here again and what a ruckus! )
beatles_small
Google has done it again. You can look at tons of pictures from LIFE magazine through Google’s LIFE photo archive. From the site:
Search millions of photographs from the LIFE photo archive, stretching from the 1750s to today. Most were never published and are now available for the first time through the joint work of LIFE and Google.

If you prefer, you can search the photo archive through Google Images and simply add source:life (e.g. sputnik source:life). This one is really fun: woodstock source:life.